Merge pull request #59 from robinzyb/devel

raise error for not finding the pos file in dpdata md paser

cp2kdata/dpdata_plugin.py

@@ -123,7 +123,10 @@ def from_labeled_system(self, file_name, restart: bool=None, **kwargs):
         # atom_numbs not total num of atoms!
         data['energies'] = cp2kmd.energies_list * AU_TO_EV
         data['cells'] = cells
-        data['coords'] = cp2kmd.atomic_frames_list
+        if cp2kmd.atomic_frames_list is None:
+            raise ValueError("No atomic coordinates found in cp2k output, do you have *-pos-*.xyz file?")
+        else:
+            data['coords'] = cp2kmd.atomic_frames_list
         data['forces'] = cp2kmd.atomic_forces_list * AU_TO_EV/AU_TO_ANG
         if cp2kmd.has_stress():
             # note that virial = stress * volume
@@ -172,72 +175,72 @@ def get_uniq_atom_names_and_types(chemical_symbols):
 # NOTE: incomplete function, do not release!
 
 
-@Format.register("cp2kdata/md_wannier")
-class CP2KMDWannierFormat(Format):
-    def from_labeled_system(self, file_name, **kwargs):
-
-        # -- Set Basic Parameters --
-        path_prefix = file_name  # in cp2k md, file_name is directory name.
-        true_symbols = kwargs.get('true_symbols', False)
-        cells = kwargs.get('cells', None)
-        cp2k_output_name = kwargs.get('cp2k_output_name', None)
-
-        # -- start parsing --
-        print(WRAPPER)
-
-        cp2kmd = Cp2kOutput(output_file=cp2k_output_name,
-                            run_type="MD", path_prefix=path_prefix)
-
-        num_frames = cp2kmd.get_num_frames()
-
-        chemical_symbols = get_chemical_symbols_from_cp2kdata(
-            cp2koutput=cp2kmd,
-            true_symbols=true_symbols
-        )
-
-        if cells is None:
-            if cp2kmd.filename:
-                # cells = cp2kmd.get_init_cell()
-                # cells = cells[np.newaxis, :, :]
-                # cells = np.repeat(cells, repeats=num_frames, axis=0)
-                cells = cp2kmd.get_all_cells()
-            else:
-                print("No cell information, please check if your inputs are correct.")
-        elif isinstance(cells, np.ndarray):
-            if cells.shape == (3, 3):
-                cells = cells[np.newaxis, :, :]
-                cells = np.repeat(cells, repeats=num_frames, axis=0)
-            elif cells.shape == (num_frames, 3, 3):
-                pass
-            else:
-                print(
-                    "Illegal Cell Information, cells shape should be (num_frames, 3, 3) or (3, 3)")
-        else:
-            print(
-                "Illegal Cell Information, cp2kdata accepts np.ndarray as cells information")
-
-        # -- data dict collects information, and return to dpdata --
-        data = {}
-        data['atom_names'], data['atom_numbs'], data["atom_types"] = get_uniq_atom_names_and_types(
-            chemical_symbols=chemical_symbols)
-        # atom_numbs not total num of atoms!
-        data['energies'] = cp2kmd.energies_list * AU_TO_EV
-        data['cells'] = cells
-
-        # get wannier centers from wannier xyz file
-
-        cp2k_wannier_file = kwargs.get('cp2k_wannier_file', None)
-        if cp2k_wannier_file:
-            print("This is wannier center parser")
-            print("Position parsed from pos files are not used.")
-            cp2k_wannier_file = os.path.join(path_prefix, cp2k_wannier_file)
-            data['coords'] = parse_pos_xyz_from_wannier(cp2k_wannier_file)
-        else:
-            raise ValueError("Please specify the cp2k wannier file name!")
-
-        data['forces'] = cp2kmd.atomic_forces_list * AU_TO_EV/AU_TO_ANG
-        if cp2kmd.has_stress():
-            data['virials'] = cp2kmd.stress_tensor_list/EV_ANG_m3_TO_GPa
-        # print(len(data['cells']), len(data['coords']), len(data['energies']))
-        print(WRAPPER)
-        return data
+# @Format.register("cp2kdata/md_wannier")
+# class CP2KMDWannierFormat(Format):
+#     def from_labeled_system(self, file_name, **kwargs):
+
+#         # -- Set Basic Parameters --
+#         path_prefix = file_name  # in cp2k md, file_name is directory name.
+#         true_symbols = kwargs.get('true_symbols', False)
+#         cells = kwargs.get('cells', None)
+#         cp2k_output_name = kwargs.get('cp2k_output_name', None)
+
+#         # -- start parsing --
+#         print(WRAPPER)
+
+#         cp2kmd = Cp2kOutput(output_file=cp2k_output_name,
+#                             run_type="MD", path_prefix=path_prefix)
+
+#         num_frames = cp2kmd.get_num_frames()
+
+#         chemical_symbols = get_chemical_symbols_from_cp2kdata(
+#             cp2koutput=cp2kmd,
+#             true_symbols=true_symbols
+#         )
+
+#         if cells is None:
+#             if cp2kmd.filename:
+#                 # cells = cp2kmd.get_init_cell()
+#                 # cells = cells[np.newaxis, :, :]
+#                 # cells = np.repeat(cells, repeats=num_frames, axis=0)
+#                 cells = cp2kmd.get_all_cells()
+#             else:
+#                 print("No cell information, please check if your inputs are correct.")
+#         elif isinstance(cells, np.ndarray):
+#             if cells.shape == (3, 3):
+#                 cells = cells[np.newaxis, :, :]
+#                 cells = np.repeat(cells, repeats=num_frames, axis=0)
+#             elif cells.shape == (num_frames, 3, 3):
+#                 pass
+#             else:
+#                 print(
+#                     "Illegal Cell Information, cells shape should be (num_frames, 3, 3) or (3, 3)")
+#         else:
+#             print(
+#                 "Illegal Cell Information, cp2kdata accepts np.ndarray as cells information")
+
+#         # -- data dict collects information, and return to dpdata --
+#         data = {}
+#         data['atom_names'], data['atom_numbs'], data["atom_types"] = get_uniq_atom_names_and_types(
+#             chemical_symbols=chemical_symbols)
+#         # atom_numbs not total num of atoms!
+#         data['energies'] = cp2kmd.energies_list * AU_TO_EV
+#         data['cells'] = cells
+
+#         # get wannier centers from wannier xyz file
+
+#         cp2k_wannier_file = kwargs.get('cp2k_wannier_file', None)
+#         if cp2k_wannier_file:
+#             print("This is wannier center parser")
+#             print("Position parsed from pos files are not used.")
+#             cp2k_wannier_file = os.path.join(path_prefix, cp2k_wannier_file)
+#             data['coords'] = parse_pos_xyz_from_wannier(cp2k_wannier_file)
+#         else:
+#             raise ValueError("Please specify the cp2k wannier file name!")
+
+#         data['forces'] = cp2kmd.atomic_forces_list * AU_TO_EV/AU_TO_ANG
+#         if cp2kmd.has_stress():
+#             data['virials'] = cp2kmd.stress_tensor_list/EV_ANG_m3_TO_GPa
+#         # print(len(data['cells']), len(data['coords']), len(data['energies']))
+#         print(WRAPPER)
+#         return data

cp2kdata/output.py

@@ -394,8 +394,8 @@ def parse_md(self):
             # if no pos file and ener file, parse energies from the output file
             format_logger(info="Energies", filename=self.filename)
             self.energies_list = parse_energies_list(self.output_file)
-
             self.energies_list = self.drop_last_info(self.cp2k_info, self.energies_list)
+            self.atomic_frames_list = None
 
         frc_xyz_file_list = glob.glob(
             os.path.join(self.path_prefix, "*frc*.xyz"))